Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so I want to know your any suggestions and corrections in my mdp files (below), so that i can use the corrected mdp file to simulate the system.
*1st mdp file :* title = Bilayer-500 cpp = /lib/cpp constraints = all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 2000000 ; 4 ns nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist = 10 ; long range interactions coulombtype = PME rlist = 1.2; neighborlist cut-off rcoulomb = 1.2; Coulomb cut-off rvdw = 1.2; VdW cut-off fourierspacing = 0.12; The maximum grid spacing for the FFT grid when using PPPM or PME pme_order = 4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 gen_vel = yes gen_temp = 303.0 gen_seed = 478905 2nd mdp file: title = Bilayer-500 cpp = /lib/cpp constraints = all-bonds integrator = md; A leap-frog algorithm for integrating Newton's equations of motion dt = 0.002 tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) nsteps = 2000000 ; 4 ns nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstxtcout = 500 xtc_precision = 1000 nstlog = 500 nstenergy = 500 nstlist = 10 ; long range interactions rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein POP SOL ref_t = 303 303 303 ; Energy monitoring energygrps = protein POP SOL ; pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 gen_vel = yes gen_temp = 303.0 gen_seed = 478905 Your help is highly appreciated. Thanks Pramod
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